Abstract Background During the SARS-CoV-2 pandemic, German early childhood education and care (ECEC) centres organised children’s attendance in different ways, they reduced opening hours, provided emergency support for a few children, or closed completely. Further, protection and hygiene measures like fixed children-staff groups, ventilation and surface disinfection were introduced in ECEC centres. To inform or modify public health measures in ECEC, we investigate the occurrence of SARS-CoV-2 infections among children and staff in ECEC centres in light of social determinants (i.e. the socioeconomic status of the children) and recommended structural and hygiene measures. We focus on the question if the relevant factors differ between the 2nd (when no variant of concern (VOC) circulated) and the 3rd wave (when VOC B.1.1.7 (Alpha) predominated). Methods Based on panel data from a weekly online survey of ECEC centre managers (calendar week 36/2020 to 22/2021, ongoing) including approx. 8500 centres, we estimate the number of SARS-CoV-2 infections in children and staff using random-effect-within-between (REWB) panel models for count data in the 2nd and 3rd wave. Results ECEC centres with a high proportion of children with low socioeconomic status (SES) have a higher risk of infections in staff and children. Strict contact restrictions between groups like fixed group assignments for children and fixed staff assignments to groups prevent infections. Both effects tend to be stronger in the 3rd wave. Conclusion ECEC centres with a large proportion of children with a low SES background and lack of using fixed child/staff cohorts experience higher COVID-19 rates. Over the long run, centres should be supported in maintaining recommended measures. Preventive measures such as the vaccination of staff should be prioritised in centres with large proportions of low SES children.